Merge pull request #11 from nutriverse/dev

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nutriverse · Apr 9, 2024 · 8dcfd6c · 8dcfd6c
2 parents 84c212b + 6da797c
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Showing 22 changed files with 183 additions and 97 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +47,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -31,20 +31,20 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,4 @@
 .Ruserdata
 .DS_Store
 inst/doc
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: anthrocheckr
 Type: Package
 Title: Anthropometric Measurement Standardisation Tests
-Version: 0.1.0
+Version: 0.0.0.9000
 Authors@R: person(given = "Ernest", 
                   family = "Guevarra", 
                   comment = c(ORCID = "0000-0002-4887-4415"), 
@@ -26,13 +26,14 @@ Suggests:
     openxlsx,
     shinydashboard,
     spelling,
-    testthat,
+    testthat (>= 3.0.0),
     dplyr,
     covr
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://nutriverse.io/anthrocheckr/, https://github.com/nutriverse/anthrocheckr
 BugReports: https://github.com/nutriverse/anthrocheckr/issues
 VignetteBuilder: knitr
+Config/testthat/edition: 3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,3 @@
-# anthrocheckr v0.1.0
+# anthrocheckr v0.0.0.9000
 
-This is the first CRAN release of `anthrocheckr`.
+This is a pre-release of `anthrocheckr`.
diff --git a/R/00_anthrocheckr.R b/R/00_anthrocheckr.R
@@ -1,5 +1,5 @@
-################################################################################
-#
+#'
+#' An Implementation of Anthropometric Measurement Standardisation Tests
 #'
 #' Ensuring the precision and accuracy of measurements is critical when
 #' collecting anthropometric data. Anthropometrists are usually tested for
@@ -15,6 +15,4 @@
 #' @importFrom shiny runApp
 #' @importFrom methods is
 #'
-#
-################################################################################
 "_PACKAGE"
diff --git a/R/01_summary_measure.R b/R/01_summary_measure.R
@@ -1,5 +1,3 @@
-################################################################################
-#
 #'
 #' Calculate the mean, sd and maximum difference value of
 #' measurements/observations
@@ -59,8 +57,6 @@
 #' @rdname calculate_summary
 #' @export
 #'
-#
-################################################################################
 
 calculate_mean <- function(measures, index = NULL) {
   if (is.null(index)) {
@@ -75,14 +71,10 @@ calculate_mean <- function(measures, index = NULL) {
 }
 
 
-################################################################################
-#
 #'
 #' @rdname calculate_summary
 #' @export
 #'
-#
-################################################################################
 
 calculate_sd <- function(measures, index = NULL) {
   if (is.null(index)) {
@@ -96,14 +88,10 @@ calculate_sd <- function(measures, index = NULL) {
 }
 
 
-################################################################################
-#
 #'
 #' @rdname calculate_summary
 #' @export
 #'
-#
-################################################################################
 
 calculate_max <- function(measures, index = NULL) {
   if (is.null(index)) {

diff --git a/R/02_calculate_tem.R b/R/02_calculate_tem.R
@@ -1,5 +1,3 @@
-################################################################################
-#
 #'
 #' Calculate technical error of measurement (TEM)
 #'
@@ -26,8 +24,6 @@
 #'
 #' @export
 #'
-#
-################################################################################
 
 calculate_tem <- function(d, n) {
   ## TEM formula

diff --git a/R/03_calculate_tem_cohort.R b/R/03_calculate_tem_cohort.R
@@ -1,5 +1,3 @@
-################################################################################
-#
 #'
 #' Calculate intra-observer TEM for each observer
 #'
@@ -33,8 +31,6 @@
 #'
 #' @export
 #'
-#
-################################################################################
 
 calculate_tem_cohort <- function(df, m1, m2, index = NULL, n) {
   ## Check that m1 is a numeric vector
@@ -48,10 +44,12 @@ calculate_tem_cohort <- function(df, m1, m2, index = NULL, n) {
   }
 
   ## get TEM
-  tem <- tapply(X = df[[m1]] - df[[m2]],
-                INDEX = df[ , index],
-                FUN = calculate_tem,
-                n = n)
+  tem <- tapply(
+    X = df[[m1]] - df[[m2]],
+    INDEX = df[ , index],
+    FUN = calculate_tem,
+    n = n
+  )
 
   ## Create data.frame
   tem <- as.data.frame.table(tem)

diff --git a/R/04_calculate_team_tem.R b/R/04_calculate_team_tem.R
@@ -1,5 +1,3 @@
-################################################################################
-#
 #'
 #' Calculate technical error of measurement (TEM) for two or more observers
 #'
@@ -20,8 +18,6 @@
 #'
 #' @export
 #'
-#
-################################################################################
 
 calculate_team_tem <- function(n, k, m) {
 

diff --git a/R/05_calculate_relative_tem.R b/R/05_calculate_relative_tem.R
@@ -1,5 +1,3 @@
-################################################################################
-#
 #'
 #' Calculate relative TEM of measurements by multiple observers.
 #'
@@ -29,8 +27,6 @@
 #'
 #' @export
 #'
-#
-################################################################################
 
 calculate_relative_tem <- function(tem, mean_value) {
   ## Calculate relative TEM
@@ -39,8 +35,3 @@ calculate_relative_tem <- function(tem, mean_value) {
   ## Return output
   return(relative_tem)
 }
-
-
-
-
-
diff --git a/R/06_calculate_total_tem.R b/R/06_calculate_total_tem.R
@@ -1,5 +1,3 @@
-################################################################################
-#
 #'
 #' Calculate the Total TEM given individual intra-observer TEM.
 #'
@@ -33,12 +31,10 @@
 #'
 #' @export
 #'
-#
-################################################################################
 
 calculate_total_tem <- function(intra, inter) {
   ## Get total TEM
-  total_tem <- sqrt((sum(intra ^ 2) / length(intra)) + (inter ^ 2)  )
+  total_tem <- sqrt((sum(intra ^ 2) / length(intra)) + (inter ^ 2))
 
   ## Return output
   return(total_tem)

diff --git a/R/07_calculate_coeff_r.R b/R/07_calculate_coeff_r.R
@@ -1,5 +1,3 @@
-################################################################################
-#
 #'
 #' Calculate the coefficient of reliability (R).
 #'
@@ -41,8 +39,6 @@
 #'
 #' @export
 #'
-#
-################################################################################
 
 calculate_coeff_r <- function(total_tem, sd) {
 

diff --git a/R/08_estimate_bias.R b/R/08_estimate_bias.R
@@ -1,5 +1,3 @@
-################################################################################
-#
 #'
 #' Calculate bias of a measurement
 #'
@@ -29,8 +27,6 @@
 #'
 #' @export
 #'
-#
-################################################################################
 
 estimate_bias <- function(msur, msup, mall) {
   ## Bias from supervisor

diff --git a/README.Rmd b/README.Rmd
@@ -12,7 +12,7 @@ knitr::opts_chunk$set(
   out.width = "100%"
 )
 ```
-# anthrocheckr: An Implementation of Anthropometric Measurement Standardisation Tests in R <img src="man/figures/logo.png" width="200" align="right" />
+# anthrocheckr: An Implementation of Anthropometric Measurement Standardisation Tests <img src="man/figures/logo.png" width="200" align="right" />
 
 <!-- badges: start -->
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
@@ -21,31 +21,38 @@ knitr::opts_chunk$set(
 [![CRAN](https://img.shields.io/cran/l/anhtrocheckr.svg)](https://CRAN.R-project.org/package=anhtrocheckr)
 [![CRAN](http://cranlogs.r-pkg.org/badges/anhtrocheckr)](https://CRAN.R-project.org/package=anhtrocheckr)
 [![CRAN](http://cranlogs.r-pkg.org/badges/grand-total/anhtrocheckr)](https://CRAN.R-project.org/package=anhtrocheckr)
-[![R build status](https://github.com/nutriverse/anthrocheckr/workflows/R-CMD-check/badge.svg)](https://github.com/nutriverse/anthrocheckr/actions)
+[![R-CMD-check](https://github.com/nutriverse/anthrocheckr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nutriverse/anthrocheckr/actions/workflows/R-CMD-check.yaml)
 [![R build status](https://github.com/nutriverse/anthrocheckr/workflows/test-coverage/badge.svg)](https://github.com/nutriverse/anthrocheckr/actions)
 [![Codecov test coverage](https://codecov.io/gh/nutriverse/anthrocheckr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/nutriverse/anthrocheckr?branch=main)
 [![CodeFactor](https://www.codefactor.io/repository/github/nutriverse/anthrocheckr/badge)](https://www.codefactor.io/repository/github/nutriverse/anthrocheckr)
-[![R-CMD-check](https://github.com/nutriverse/anthrocheckr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nutriverse/anthrocheckr/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 Ensuring the precision and accuracy of measurements is critical when collecting anthropometric data. Anthropometrists are usually tested for precision and accuracy of measurement through standardisation tests performed prior to anthropometric data collection. This package provides functions to calculate inter- and intra-observer technical error of measurement (TEM) to assess precision of measurements.
 
-## Installation
+## What does `anthrocheckr` do?
 
-`anthrocheckr` is still in active development and is not available on [CRAN](https://cran.r-project.org/) yet.
+## Installation
 
-You can install the development version of `anthrocheckr` from [GitHub](https://github.com/nutriverse/anthrocheckr) with:
+`anthrocheckr` is not yet on [CRAN](https://cran.r-project.org) but can be installed from the [nutriverse R universe](https://nutriverse.r-universe.dev) as follows:
 
-```{r install_github, echo = TRUE, eval = FALSE}
-if(!require(remotes)) install.packages("remotes")
-remotes::install_github("nutriverse/anthrocheckr")
+```{r install-r-universe, eval = FALSE}
+install.packages(
+  "anthrocheckr",
+  repos = c('https://nutriverse.r-universe.dev', 'https://cloud.r-project.org')
+)
 ```
 
 ## Usage
 
 
 
+## Citation
+
+If you find the `anthrocheckr` package useful please cite using the suggested citation provided by a call to the `citation()` function as follows:
 
+```{r citation}
+citation("anthrocheckr")
+```
 
 ## Community guidelines